Document Detail


Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index.
MedLine Citation:
PMID:  18753218     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Classification of viral sequences should be fast, objective, accurate and reproducible. Most methods that classify sequences use either pair-wise distances or phylogenetic relations, but cannot discern when a sequence is unclassifiable. The branching index (BI) combines distance and phylogeny methods to compute a ratio that quantifies how closely a query sequence clusters with a subtype clade. In the hypothesis-testing framework of statistical inference, the BI is compared with a threshold to test whether sufficient evidence exists for the query sequence to be classified among known sequences. If above the threshold, the null hypothesis of no support for the subtype relation is rejected and the sequence is taken as belonging to the subtype clade with which it clusters on the tree. This study evaluates statistical properties of the BI for subtype classification in hepatitis C virus (HCV) and human immunodeficiency virus-1 (HIV-1). Pairs of BI values with known positive- and negative-test results were computed from 10,000 random fragments of reference alignments. Sampled fragments were of sufficient length to contain phylogenetic signals that grouped reference sequences together properly into subtype clades. For HCV, a threshold BI of 0.71 yields 95.1% agreement with reference subtypes, with equal false-positive and false-negative rates. For HIV-1, a threshold of 0.66 yields 93.5% agreement. Higher thresholds can be used where lower false-positive rates are required. In synthetic recombinants, regions without breakpoints are recognized accurately; regions with breakpoints do not represent any known subtype uniquely. Web-based services for viral subtype classification with the BI are available online.
Authors:
Peter Hraber; Carla Kuiken; Mark Waugh; Shaun Geer; William J Bruno; Thomas Leitner
Related Documents :
9171218 - Isolation and characterization of two divergent infectious molecular clones of hiv type...
11172098 - Re-analysis of human immunodeficiency virus type 1 isolates from cyprus and greece, ini...
9791018 - Macaques infected with cloned simian immunodeficiency virus show recurring nef gene alt...
17189978 - Three type 6 hepatitis c virus subgroups among blood donors in the yangon area of myanm...
22843578 - Draft genome sequence of corynebacterium bovis dsm 20582, which causes clinical mastiti...
11101668 - Prochlorococcus marinus strain pcc 9511, a picoplanktonic cyanobacterium, synthesizes t...
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  The Journal of general virology     Volume:  89     ISSN:  0022-1317     ISO Abbreviation:  J. Gen. Virol.     Publication Date:  2008 Sep 
Date Detail:
Created Date:  2008-08-28     Completed Date:  2008-09-30     Revised Date:  2013-06-05    
Medline Journal Info:
Nlm Unique ID:  0077340     Medline TA:  J Gen Virol     Country:  England    
Other Details:
Languages:  eng     Pagination:  2098-107     Citation Subset:  IM    
Affiliation:
Theoretical Biology & Biophysics, T-10 MS K710, LANL, Los Alamos, NM 87545, USA. phraber@lanl.gov
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Genetic Variation
Genome, Viral
HIV-1 / classification*,  genetics*
Hepacivirus / classification*,  genetics*
Humans
Phylogeny
Recombination, Genetic
Grant Support
ID/Acronym/Agency:
Y01 AI1500/AI/NIAID NIH HHS; Y1-AI-1500-01/AI/NIAID NIH HHS
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  Identification of HLA-A*01- and HLA-A*02-restricted CD8+ T-cell epitopes shared among group B entero...
Next Document:  Establishment of an infectious genotype 1b hepatitis C virus clone in human hepatocyte chimeric mice...